2yma: Difference between revisions

Revision as of 14:05, 1 February 2024

X-ray structure of the Yos9 dimerization domain

Structural highlights

2yma is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.545Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OS9_YEAST Lectin involved in the quality control of the secretory pathway. As a member of the endoplasmic reticulum-associated degradation lumenal (ERAD-L) surveillance system, targets misfolded endoplasmic reticulum lumenal glycoproteins for degradation. The recognition of targets is N-glycan specific.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

In yeast, the membrane-bound HMG-CoA reductase degradation (HRD) ubiquitin-ligase complex is a key player of the ER-associated protein degradation pathway that targets misfolded proteins for proteolysis. Yos9, a component of the luminal submodule of the ligase, scans proteins for specific oligosaccharide modifications, which constitute a critical determinant of the degradation signal. Here, we report the crystal structure of the Yos9 domain that was previously suggested to confer binding to Hrd3, another component of the HRD complex. We observe an alphabeta-roll domain architecture and a dimeric assembly which are confirmed by analytical ultracentrifugation of both the crystallized domain and full-length Yos9. Our binding studies indicate that, instead of this domain, the N-terminal part of Yos9 including the mannose 6-phosphate receptor homology domain mediates the association with Hrd3 in vitro. Our results support the model of a dimeric state of the HRD complex and provide first-time evidence of self-association on its luminal side.

Structural and Biochemical Basis of Yos9 Protein Dimerization and Possible Contribution to Self-association of 3-Hydroxy-3-methylglutaryl-Coenzyme A Reductase Degradation Ubiquitin-Ligase Complex.,Hanna J, Schutz A, Zimmermann F, Behlke J, Sommer T, Heinemann U J Biol Chem. 2012 Mar 9;287(11):8633-40. Epub 2012 Jan 18. PMID:22262864^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Friedmann E, Salzberg Y, Weinberger A, Shaltiel S, Gerst JE. YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem. 2002 Sep 20;277(38):35274-81. Epub 2002 Jun 20. PMID:12077121 doi:https://dx.doi.org/10.1074/jbc.M201044200
↑ Buschhorn BA, Kostova Z, Medicherla B, Wolf DH. A genome-wide screen identifies Yos9p as essential for ER-associated degradation of glycoproteins. FEBS Lett. 2004 Nov 19;577(3):422-6. PMID:15556621 doi:https://dx.doi.org/S0014579304012773
↑ Bhamidipati A, Denic V, Quan EM, Weissman JS. Exploration of the topological requirements of ERAD identifies Yos9p as a lectin sensor of misfolded glycoproteins in the ER lumen. Mol Cell. 2005 Sep 16;19(6):741-51. PMID:16168370 doi:https://dx.doi.org/S1097-2765(05)01524-8
↑ Kim W, Spear ED, Ng DT. Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell. 2005 Sep 16;19(6):753-64. PMID:16168371 doi:https://dx.doi.org/S1097-2765(05)01528-5
↑ Szathmary R, Bielmann R, Nita-Lazar M, Burda P, Jakob CA. Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell. 2005 Sep 16;19(6):765-75. PMID:16168372 doi:https://dx.doi.org/S1097-2765(05)01557-1
↑ Hanna J, Schutz A, Zimmermann F, Behlke J, Sommer T, Heinemann U. Structural and Biochemical Basis of Yos9 Protein Dimerization and Possible Contribution to Self-association of 3-Hydroxy-3-methylglutaryl-Coenzyme A Reductase Degradation Ubiquitin-Ligase Complex. J Biol Chem. 2012 Mar 9;287(11):8633-40. Epub 2012 Jan 18. PMID:22262864 doi:10.1074/jbc.M111.317644

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Friedmann E, Salzberg Y, Weinberger A, Shaltiel S, Gerst JE. YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem. 2002 Sep 20;277(38):35274-81. Epub 2002 Jun 20. PMID:12077121 doi:https://dx.doi.org/10.1074/jbc.M201044200

[2] Buschhorn BA, Kostova Z, Medicherla B, Wolf DH. A genome-wide screen identifies Yos9p as essential for ER-associated degradation of glycoproteins. FEBS Lett. 2004 Nov 19;577(3):422-6. PMID:15556621 doi:https://dx.doi.org/S0014579304012773

[3] Bhamidipati A, Denic V, Quan EM, Weissman JS. Exploration of the topological requirements of ERAD identifies Yos9p as a lectin sensor of misfolded glycoproteins in the ER lumen. Mol Cell. 2005 Sep 16;19(6):741-51. PMID:16168370 doi:https://dx.doi.org/S1097-2765(05)01524-8

[4] Kim W, Spear ED, Ng DT. Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell. 2005 Sep 16;19(6):753-64. PMID:16168371 doi:https://dx.doi.org/S1097-2765(05)01528-5

[5] Szathmary R, Bielmann R, Nita-Lazar M, Burda P, Jakob CA. Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell. 2005 Sep 16;19(6):765-75. PMID:16168372 doi:https://dx.doi.org/S1097-2765(05)01557-1

[6] Hanna J, Schutz A, Zimmermann F, Behlke J, Sommer T, Heinemann U. Structural and Biochemical Basis of Yos9 Protein Dimerization and Possible Contribution to Self-association of 3-Hydroxy-3-methylglutaryl-Coenzyme A Reductase Degradation Ubiquitin-Ligase Complex. J Biol Chem. 2012 Mar 9;287(11):8633-40. Epub 2012 Jan 18. PMID:22262864 doi:10.1074/jbc.M111.317644

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='2yma' size='340' side='right'caption='[[2yma]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yma]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YMA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yma]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YMA FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yma OCA], [https://pdbe.org/2yma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yma RCSB], [https://www.ebi.ac.uk/pdbsum/2yma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yma ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.545&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yma OCA], [https://pdbe.org/2yma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yma RCSB], [https://www.ebi.ac.uk/pdbsum/2yma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yma ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/OS9_YEAST OS9_YEAST]] Lectin involved in the quality control of the secretory pathway. As a member of the endoplasmic reticulum-associated degradation lumenal (ERAD-L) surveillance system, targets misfolded endoplasmic reticulum lumenal glycoproteins for degradation. The recognition of targets is N-glycan specific.<ref>PMID:12077121</ref> <ref>PMID:15556621</ref> <ref>PMID:16168370</ref> <ref>PMID:16168371</ref> <ref>PMID:16168372</ref>
+[https://www.uniprot.org/uniprot/OS9_YEAST OS9_YEAST] Lectin involved in the quality control of the secretory pathway. As a member of the endoplasmic reticulum-associated degradation lumenal (ERAD-L) surveillance system, targets misfolded endoplasmic reticulum lumenal glycoproteins for degradation. The recognition of targets is N-glycan specific.<ref>PMID:12077121</ref> <ref>PMID:15556621</ref> <ref>PMID:16168370</ref> <ref>PMID:16168371</ref> <ref>PMID:16168372</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Behlke, J]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Hanna, J]]
+[[Category: Behlke J]]
-[[Category: Heinemann, U]]
+[[Category: Hanna J]]
-[[Category: Schuetz, A]]
+[[Category: Heinemann U]]
-[[Category: Sommer, T]]
+[[Category: Schuetz A]]
-[[Category: Zimmermann, F]]
+[[Category: Sommer T]]
-[[Category: Carbohydrate binding protein]]
+[[Category: Zimmermann F]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Endoplasmic reticulum-associated protein degradation]]
-[[Category: Hrd complex]]
-[[Category: Misfolded protein]]
-[[Category: Quality control]]

2yma: Difference between revisions

Revision as of 14:05, 1 February 2024

X-ray structure of the Yos9 dimerization domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools